On aggregation in multiset-based self-assembly of graphs |
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Authors: | Francesco Bernardini Robert Brijder Matteo Cavaliere Giuditta Franco Hendrik Jan Hoogeboom Grzegorz Rozenberg |
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Affiliation: | (1) Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands;(2) The Microsoft Research-University of Trento, Centre for Computational and Systems Biology (CoSBi), Trento, Italy;(3) Department of Computer Science, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; |
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Abstract: | We continue the formal study of multiset-based self-assembly. The process of self-assembly of graphs, where iteratively new
nodes are attached to a given graph, is guided by rules operating on nodes labelled by multisets. In this way, the multisets
and rules model connection points (such as “sticky ends”) and complementarity/affinity between connection points, respectively.
We identify three natural ways (individual, free, and collective) to attach (aggregate) new nodes to the graph, and study
the generative power of the corresponding self-assembly systems. For example, it turns out that individual aggregation can
be simulated by free or collective aggregation. However, we demonstrate that, for a fixed set of connection points, collective
aggregation is rather restrictive. We also give a number of results that are independent of the way that aggregation is performed. |
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